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Rationale: Stable isotope analysis (SIA) is a powerful tool to estimate dietary links between polar zooplankton. However, the presence of highly variable 12C‐rich lipids may skew estimations as they are depleted in 13C relative to proteins and carbohydrates, consequently masking carbon signals from food sources. Lipid effects on pteropod‐specific values requires examining, since accounting for lipids is rarely conducted among the few existing pteropod‐related SIA studies. It is currently unclear whether lipid correction is necessary prior to SIA of pteropods. Methods: Whole bodies of three species of pteropods (Clio pyramidata f. sulcata, Clione limacina antarctica, and Spongiobranchaea australis) sampled from the Southern Ocean were lipid‐extracted chemically to test the effects on δ13C and δ15N values (n = 38 individuals in total). We determined the average change in δ13C values for each treatment, and compared this offset with those from published normalization models. We tested lipid correction effects on isotopic niche dispersion metrics to compare interpretations surrounding food web dynamics. Results: Pteropods with lipids removed had δ13C values up to 4.5‰ higher than bulk samples. However, lipid extraction also produced higher δ15N values than bulk samples. Isotopic niche overlaps between untreated pteropods and their potential food sources were significantly different from overlaps generated between lipid‐corrected pteropods and their potential food sources. Data converted using several published normalization models did not reveal significant differences among various calculated niche metrics, including standard ellipse and total area. Conclusions: We recommend accounting for lipids via chemical extraction or mathematical normalization before applying SIA to calculate ecological niche metrics, particularly for organisms with moderate to high lipid content such as polar pteropods. Failure to account for lipids may result in misinterpretations of niche dimensions and overlap and, consequently, trophic interactions. [ABSTRACT FROM AUTHOR]